User's Guide S I E S T A 3.2 March 24, 2013 Emilio Artacho University of Cambridge Jos´eMar´ıaCela Barcelona Supercomputing Center Julian D. Gale Curtin University of Technology, Perth Alberto Garc´ıa Institut de Ci`enciade Materials, CSIC, Barcelona Javier Junquera Universidad de Cantabria, Santander Richard M. Martin University of Illinois at Urbana-Champaign Pablo Ordej´on Centre de Investigaci´oen Nanoci`encia i Nanotecnologia, (CSIC-ICN), Barcelona Daniel S´anchez-Portal Unidad de F´ısica de Materiales, Centro Mixto CSIC-UPV/EHU, San Sebasti´an Jos´eM. Soler Universidad Aut´onomade Madrid http://www.uam.es/siesta Copyright c Fundaci´onGeneral Universidad Aut´onomade Madrid: E.Artacho, J.D.Gale, A.Garc´ıa,J.Junquera, P.Ordej´on,D.S´anchez-Portal and J.M.Soler, 1996-2013 Contents 1 INTRODUCTION 5 2 COMPILATION 7 2.1 The building directory . 7 2.1.1 Multiple-target compilation . 8 2.2 The arch.make file . 8 3 EXECUTION OF THE PROGRAM 9 4 THE FLEXIBLE DATA FORMAT (FDF) 11 5 PROGRAM OUTPUT 12 5.1 Standard output . 12 5.2 Output to dedicated files . 13 6 DETAILED DESCRIPTION OF PROGRAM OPTIONS 14 6.1 General system descriptors . 14 6.2 Pseudopotentials . 15 6.3 Basis set and KB projectors . 16 6.3.1 Overview of atomic-orbital bases implemented in Siesta . 16 6.3.2 Type of basis sets . 20 6.3.3 Size of the basis set . 20 6.3.4 Range of the orbitals . 21 6.3.5 Generation of multiple-zeta orbitals . 21 6.3.6 Soft-confinement options . 22 6.3.7 Kleinman-Bylander projectors . 23 6.3.8 The PAO.Basis block . 24 6.3.9 Filtering . 27 6.3.10 Saving and reading basis-set information . 27 6.3.11 Tools to inspect the orbitals and KB projectors . 28 6.3.12 Basis optimization . 28 6.3.13 Low-level options regarding the radial grid . 28 6.4 Structural information . 30 6.4.1 Traditional structure input in the fdf file . 30 1 6.4.2 Z-matrix format and constraints . 32 6.4.3 Output of structural information . 36 6.4.4 Input of structural information from external files . 38 6.4.5 Input from a FIFO file . 39 6.4.6 Precedence issues in structural input . 39 6.4.7 Interatomic distances . 39 6.5 k-point sampling . 39 6.5.1 Output of k-point information . 41 6.6 Exchange-correlation functionals . 41 6.7 Spin polarization . 42 6.8 The self-consistent-field loop . 43 6.8.1 Mixing options . 44 6.8.2 Initialization of the density-matrix . 45 6.8.3 Initialization of the SCF cycle with charge densities . 48 6.8.4 Output of density matrix . 48 6.8.5 Convergence criteria . 49 6.9 The real-space grid and the eggbox-effect . 50 6.10 Matrix elements of the Hamiltonian and overlap . 53 6.10.1 The auxiliary supercell . 54 6.11 Calculation of the electronic structure . 54 6.11.1 Diagonalization options . 55 6.11.2 Output of eigenvalues and wavefunctions . 56 6.11.3 Occupation of electronic states and Fermi level . 57 6.11.4 Order(N) calculations . 58 6.12 Band-structure analysis . 61 6.12.1 Format of the .bands file . 62 6.12.2 Output of wavefunctions associated to bands . 62 6.13 Output of selected wavefunctions . 63 6.14 Densities of states . 64 6.14.1 Total density of states . 64 6.14.2 Partial (projected) density of states . 65 6.14.3 Local density of states . 66 6.15 Options for chemical analysis . 66 6.15.1 Mulliken charges and overlap populations . 66 2 6.15.2 Voronoi and Hirshfeld atomic population analysis . 67 6.15.3 Crystal-Orbital overlap and hamilton populations (COOP/COHP) . 68 6.16 Optical properties . 69 6.17 Macroscopic polarization . 70 6.18 Systems with net charge or dipole, and electric fields . 73 6.19 Output of charge densities and potentials on the grid . 74 6.20 Auxiliary Force field . 76 6.21 Parallel options . 78 6.21.1 Parallel decompositions for O(N) . 79 6.22 Efficiency options . 79 6.23 Memory accounting options . 80 6.24 The catch-all option UseSaveData . 80 6.25 Output of information for Denchar . 80 7 STRUCTURAL RELAXATION, PHONONS, AND MOLECULAR DY- NAMICS 81 7.1 Structural relaxation . 82 7.1.1 Conjugate-gradients optimization . 84 7.1.2 Broyden optimization . 84 7.1.3 FIRE relaxation . 85 7.1.4 Quenched MD . 85 7.2 Target stress options . 86 7.3 Molecular dynamics . 87 7.4 Output options for dynamics . 88 7.5 Restarting geometry optimizations and MD runs . 90 7.6 Use of general constraints . 90 7.7 Phonon calculations . 92 7.8 Interface to the PHONON program . 93 8 TRANSIESTA 94 8.1 Brief description . 94 8.2 Source code structure . 94 8.3 Compilation . 95 8.4 Running a fast example . 95 8.5 Brief explanation . 96 3 8.6 Electrodes . 97 8.7 TranSiesta Options . 98 8.7.1 General options . 98 8.7.2 Electrode description options . 99 8.7.3 Complex contour integration options . 100 8.7.4 Bias contour integration options . 100 8.8 Matching TranSiesta coordinates: basic rules . 101 8.9 Output . 101 8.10 Utilities for analysis: tbtrans. ............................102 8.10.1 Compiling TBTtrans . 103 9 ANALYSIS TOOLS 103 10 SCRIPTING 103 11 PROBLEM HANDLING 104 11.1 Error and warning messages . 104 11.2 Known but unsolved problems and bugs . 104 12 REPORTING BUGS 105 13 ACKNOWLEDGMENTS 105 14 APPENDIX: Physical unit names recognized by FDF 106 15 APPENDIX: NetCDF 108 16 APPENDIX: Parallel Siesta 110 17 APPENDIX: File Formats 113 18 APPENDIX: XML Output 115 18.1 Controlling XML output . 115 18.2 Converting XML to XHTML . 116 19 APPENDIX: Selection of precision for storage 117 Index 117 4 1 INTRODUCTION This Reference Manual contains descriptions of all the input, output and execution features of Siesta, but is not really a tutorial introduction to the program. The development team is planning a documentation overhaul that will address this shortcoming. In the meantime, interested users can find tutorial material prepared for Siesta schools and workshops at the project's web page http://www.uam.es/siesta Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and.